Found 123 structures.
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1. Compound ID: 183
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R-3HOBut-(1-5)-a-Psep7Fo-(2-4)-b-D-Xylp-(1-3)-b-D-FucpNAc-(1-3)-L-Ser |
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Structure type: oligomer
Trivial name: pilin glycan
Contained glycoepitopes: IEDB_114701,IEDB_150900,IEDB_167188,IEDB_174332
The structure is contained in the following publication(s):
- Article ID: 38
Castric P, Cassels FJ, Carlson RW "Structural characterization of the Pseudomonas aeruginosa 1244 pilin glycan" -
Journal of Biological Chemistry 276(28) (2001) 26479-26485
An antigenic similarity between lipopolysaccharide (LPS) and glycosylated pilin of Pseudomonas aeruginosa 1244 was noted. We purified a glycan-containing molecule from proteolytically digested pili and showed it to be composed of three sugars and serine. This glycan competed with pure pili and LPS for reaction with an LPS-specific monoclonal antibody, which also inhibited twitching motility by P. aeruginosa bearing glycosylated pili. One-dimensional NMR analysis of the glycan indicated the sugars to be 5N β OHC(4)7NfmPse, Xyl, and FucNAc. The complete proton assignments of these sugars as well as the serine residue were determined by COSY and TOCSY. Electrospray ionization mass spectrometry (MS) determined the mass of this molecule to be 771.5. The ROESY NMR spectrum, tandem MS/MS analysis, and methylation analysis provided information on linkage and the sequence of oligosaccharide components. These data indicated that the molecule had the following structure: α-5N β OHC(4)7NFmPse-(2→4)β-Xyl-(1→3)-β-FucNAc-(1→3)-β-Ser
structural, characterization, Pseudomonas, Pseudomonas aeruginosa, glycan, pilin, pseudaminic acid
NCBI PubMed ID: 11342554Journal NLM ID: 2985121RPublisher: Baltimore, MD: American Society for Biochemistry and Molecular Biology
Correspondence: castric@duq.edu
Institutions: Department of Biological Sciences, Duquesne University, Pittsburgh, Pennsylvania 15282, USA
Methods: 1H NMR, GLC-MS, NMR-2D, sugar analysis, ESI-MS, Western blotting, amino acid analysis, MS/MS
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2. Compound ID: 722
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Asp-(1-2)-+
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a-L-Rhap2Me-(1-4)-+ |
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b-D-GlcpNAcA4Me-(1-4)-b-D-GlcpA-(1-4)-b-D-Xylp2Ac3Ac-(1-4)-a-D-GlcpA2Me-(1-2)-a-D-Manp-(1-3)-Ser-(1-2)-Ala-(1-2)-Ala |
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Structure type: oligomer
Trivial name: glycopeptide
Contained glycoepitopes: IEDB_114701,IEDB_115136,IEDB_130701,IEDB_136105,IEDB_140630,IEDB_144983,IEDB_150900,IEDB_152206,IEDB_167188,IEDB_174332,IEDB_225177,IEDB_423153,IEDB_885823,IEDB_983930,SB_44,SB_67,SB_72
The structure is contained in the following publication(s):
- Article ID: 192
Vinogradov E, Perry MB, Kay WW "The structure of the glycopeptides from the fish pathogen Flavobacterium columnare" -
Carbohydrate Research 338(23) (2003) 2653-2658
Proteolytic digestion of the phenol-water extraction product of the fish pathogen Flavobacterium columnare afforded a mixture of glycopeptides in which the oligosaccharide moiety was an unusual hexasaccharide composed of 4-O-methyl-2-acetamido-2-deoxy-D-glucuronic acid (GlcNAcA), D-glucuronic acid (D-GlcA), 2,3-di-O-acetyl-D-xylose (D-Xyl), 2-O-methyl-D-glucuronic acid (D-GlcA), D-mannose (D-Man), and 2-O-methyl-L-rhamnose (L-Rha). By the application of high-resolution 1D and 2D NMR, mass spectrometry, and chemical analysis, the hexasaccharide structure was determined to be: [carbohydrate structure--see text] where all monosaccharides have the D-configuration except for 2-O-methyl-L-rhamnose; and were in the pyranose form. Only one carbohydrate structure was found. The peptide part was represented by tri- to hepta-peptides with a minimal common tripeptide fragment Asp-Ser-Ala, extended with Ala and Val
NMR, MS, Flavobacterium columnare, glycopeptide
NCBI PubMed ID: 14670723Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: evguenii.vinogradov@nrc-cnrc.gc.ca
Institutions: Institute for Biological Sciences, National Research Council, 100 Sussex Dr., Ottawa, ON, Canada K1A 0R6, Department of Bacteriology and Biochemistry, University of Victoria, Victoria, BC, Canada V8W 2T2
Methods: NMR-2D, NMR, chemical analysis, MS
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3. Compound ID: 1476
Structure type: oligomer
Aglycon: protein
Compound class: S-layer glycoprotein
Contained glycoepitopes: IEDB_142488,IEDB_144998,IEDB_146664,IEDB_150900,IEDB_158538,IEDB_2346541,IEDB_983931,SB_192
The structure is contained in the following publication(s):
- Article ID: 468
Schäffer C, Messner P "Surface-layer glycoproteins: an example for the diversity of bacterial glycosylation with promising impacts on nanobiotechnology" -
Glycobiology 14(8) (2004) 31R-42R
Bacterial cell surface layers, referred to simply as S-layers, have been described for all major phylogenetic groups of bacteria, which may indicate their pivotal role for a bacterium in its natural habitat. They have the unique ability to assemble into two-dimensional crystalline arrays that completely cover the bacterial cells. Glycosylation represents the most frequent modification of S-layer proteins. S-layer glycoproteins constitute a class of glycoconjugates first isolated in the mid-1970s, but S-layer glycoprotein research is still being regarded as an 'exotic field of glycobiology,' possibly because of its 'noneukaryotic' character. Extensive work over the past 30 years provided evidence of an enormous diversity of S-layer glycoproteins that have been created in nature over 3 billion years of prokaryotic evolution. These glycoconjugates are substantially different from eukaryotic glycoproteins, with regard to both composition and structure; nevertheless, some general structural concepts may be deduced. The awareness of the high application potential of S-layer glycoproteins, especially in combination with their intrinsic cell surface display feature, in the field of modern nanobiotechnology as a base for glycoengineering has recently led to the investigation of the S-layer protein glycosylation process at the molecular level, which has lagged behind the structural studies due to the lack of suitable molecular tools. From that work an even more interesting picture of this class of glycoconjugates is emerging. The availability of purified enzymes from S-layer glycan biosynthesis pathways exhibiting increased stabilities and/or rare sugar specificities in conjunction with preliminary genomic data on S-layer glycan biosynthesis clusters will pave the way for the rational design of S-layer neoglycoproteins.
LPS, bacterial glycosylation, genomic glycosylation loci, glycan diversity, glycoengineering, S-layer nanoglycobiology
NCBI PubMed ID: 15044388Publication DOI: 10.1093/glycob/cwh064Journal NLM ID: 9104124Publisher: IRL Press at Oxford University Press
Correspondence: paul.messner@boka.ac.at
Institutions: Center for NanoBiotechnology, University of Applied Life Sciences and Natural Resources, Gregor-Mendel-Strasse 33, A-1180 Wien, Austria
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4. Compound ID: 1591
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L-Lys-(2-6)-+ L-Ser-(2-6)-+
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-4)-a-D-GalpA-(1-4)-a-D-Galp-(1-3)-a-D-GalpA4Ac-(1-3)-b-D-GlcpNAc-(1- |
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Structure type: polymer chemical repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_136906,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_150900,IEDB_151528,IEDB_151531,IEDB_190606,IEDB_733911,SB_7
The structure is contained in the following publication(s):
- Article ID: 494
Torzewska A, Kocharova NA, Maszewska A, Knirel YA, Rozalski A "Serological characterization of the O-specific polysaccharide of Providencia alcalifaciens O23" -
Archivum Immunologiae et Therapiae Experimentalis 52(1) (2004) 43-49
INTRODUCTION: The genus Providencia belongs to the Enterobacteriaceae family and currently consists of five species: P. alcalifaciens, P. heimbachae, P. rettgerii, P. rustigianii and P. stuartii. The serological classification scheme of P. alcalifaciens, P. rustigianii and P. stuartii includes 63 O-serogroups and 30 H-serogroups. The O-antigenic specificity is defined by the structure of the O-antigen (O-specific polysaccharide--OPS), a part of the lipopolysaccharide (LPS, endotoxin), one of the major components of the outer membrane of gram-negative bacteria and an important virulence factor of these bacteria. Among the bacteria of the Enterobacteriaceae family, the genus Providencia is one of the least studied in respect to its LPS structure and antigenic specificity. Studies of the chemical structures and the serological specificity of the O-antigens aim at the elucidation of the molecular basis of the serological classification of Providencia sp. MATERIALS AND METHODS: LPS and alkali-treated LPS of P. alcalifaciens O23 and serologically related P. rustigianii O14, P. mirabilis O13 and P. myxofaciens as well as O-antiserum against P. alcalifaciens O23 were used. Serological characterization of P. alcalifaciens O23 O-specific polysaccharide was done by use enzyme immunosorbent assay (EIA), passive hemolysis test (PHT) as well as by inhibition and sodium deoxycholate polyacrylamide gel electrophoresis (DOC-PAGE) of LPS and Western blot. RESULTS AND CONCLUSIONS: The OPS of P. alcalifaciens, O23, contains an N-(D-glucuronoyl)-N-[(R)-1-carboxyethyl]-L-lysine residue (GlcAAlaLys). The LPS of P. alcalifaciens, O23, and other LPSs containing AlaLys from Providencia and Proteus strains were tested with rabbit anti-P. alcalifiaciens O23 serum. The serological data showed that a GlcAAlaLys-associated epitope plays a role as an antigenic determinant in the P. alcalifaciens O23 OPS and revealed the particular importance of glucuronic acid and the carboxyethyl group for the binding of O23-specific antibodies.
Lipopolysaccharide, structure, characterization, polysaccharide, O-antigen, O-specific, O-specific polysaccharide, Providencia, Providencia alcalifaciens, serological, O-serogroups, Ne-[(R)-1-carboxyethyl]-L-lysine
NCBI PubMed ID: 15053232Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: rozala@biol.uni.lodz.pl
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Institute of Microbiology and Immunology, University of Lodz, Lodz, Poland
- Article ID: 1123
Radziejewska-Lebrecht J, Shashkov AS, Grosskurth H, Bartodziejska B, Knirel YA, Vinogradov EV, Rozalski A, Kaca W, Kononov LO, Chernyak AY, Mayer H, Kochetkov NK "Structure and epitope characterisation of the O-specific polysaccharide of Proteus mirabilis O28 containing amides of D-galacturonic acid with L-serine and L-lysine" -
European Journal of Biochemistry 230 (1995) 705-712
The O-specific polysaccharide of Proteus mirabilis O28 was found to contain D-galactose, D-galacturonic acid (GalA), 2-acetamido-2-deoxy-D-glucose, L-serine, L-lysine, and O-acetyl groups in molar ratios 1:2:1:1:1:1, the amino acids being linked via their alpha-amino group to the carboxyl group of GalA. The polysaccharide was studied using 1H- and 13C NMR spectroscopy, including selective spin-decoupling, one-dimensional total correlation spectroscopy, two-dimensional homonuclear correlation spectroscopy (COSY), heteronuclear 13C,1H COSY, one-dimensional NOE, and two-dimensional rotating-frame NOE spectroscopy and partial acid hydrolysis followed by borohydride reduction, methylation, and GLC/MS analysis of the derived glycosyl alditols. The following structure of the repeating unit was established: [formula: see text] Epitope specificity of the P. mirabilis O28 polysaccharide was analysed using a homologous rabbit polyclonal antiserum in quantitative precipitation, passive immunohemolysis, and inhibition of passive immunohemolysis. Study with related synthetic glycopolymers (2-acrylamidoethyl glycosides of amides of α-D-GalA with amino acids copolymerised with acrylamide) showed the importance of D-GalA(L-Lys) for manifesting serological specificity of the O-antigen. Serological cross-reactions between P. mirabilis O28, S1959, and R14/S1959 (a transient-like form) are discussed
Lipopolysaccharide, structure, O antigen, epitope, Proteus mirabilis
NCBI PubMed ID: 7541753Journal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: knirel@ioc.ac.ru
Institutions: Institute of Microbiology and Immunology, University of Lodz, Poland
Methods: methylation, NMR-2D, partial acid hydrolysis, NMR
- Article ID: 1467
Knirel YA, Kaca W, Rozalski A, Sidorczyk Z "Structure of the O-antigenic polysaccharides of Proteus bacteria" -
Polish Journal of Chemistry 73 (1999) 895-907
Data on the composition and structure of the O-specific polysaccharides (O-antigens) of the lipopolysaccharides of the genus Proteus are summarized and discussed as the molecular basis for serotyping of these medically important bacteria.
structure, O-antigen, Proteus, Bacterial polysaccharide, epitope specificity
Journal NLM ID: 7901356WWW link: http://www.ichf.edu.pl/pjch/pj-1999/pj0699.htm#0895Publisher: Państwowe Wydawnictwo Naukowe
Correspondence: knirel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences,Leninsky Prospekt 47, Moscow, Russia, Institute of Microbiology and Immunology, University of Łódź, Banacha 12/16, 90-237 Łódź, Poland, Center of Microbiology and Virology, Polish Academy of Sciences, Lodowa 106, 93-232 Łódź, Poland
- Article ID: 4802
Siwinska M, Levina EA, Ovchinnikova OG, Drzewiecka D, Shashkov AS, Rozalski A, Knirel YA "Classification of a Proteus penneri clinical isolate with a unique O-antigen structure to a new Proteus serogroup, O80" -
Carbohydrate Research 407 (2015) 131-136
Proteus penneri is an opportunistic pathogen, which may cause severe diseases, most frequently urinary tract infections in immunocompromised patients. P. penneri Br 114 exhibiting a good swarming growth ability as an S-form strain was isolated from a wound of a patient in Lodz, Poland. Serological studies using ELISA and Western blotting and chemical analyses along with (1)H and (13)C NMR spectroscopy showed that the O-antigen (O-polysaccharide) of this strain is unique among the known Proteus serotypes O1-O79. It possesses a linear pentasaccharide repeating unit containing a partially O-acetylated amide of D-glucuronic acid (GlcA) with L-serine having the following structure: [structure: see text]. These data are a basis for creating a new Proteus serogroup, O80, so far represented by the single Br 114 isolate. The O80 is the 21st O-serogroup containing P. penneri strains and the fourth serogroup based on Proteus spp. clinical isolates from Lodz, Poland.
Lipopolysaccharide, O-antigen, Proteus penneri, serological classification, bacterial polysaccharide structure
NCBI PubMed ID: 25771295Publication DOI: 10.1016/j.carres.2015.02.003Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: domkam@biol.uni.lodz.pl
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Department of General Microbiology, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, 90-237 Łódź, Poland, Higher Chemical College of the Russian Academy of Sciences, 125047 Moscow, Russia, Department of Immunobiology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, 90-237 Łódź, Poland
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, SDS-PAGE, ELISA, GLC, mild acid hydrolysis, Western blotting, de-O-acetylation, composition analysis, GPC
- Article ID: 6050
Drzewiecka D, Palusiak A, Siwinska M, Zablotni A "The prevailing O serogroups among the serologically differentiated clinical Proteus spp. strains in central Poland" -
Scientific Reports 11(1) (2021) 18982
In the years 2006-2011, 617 Proteus spp. strains isolated mostly from urine and wounds or other clinical sources were collected in Lodz, Poland, to determine the offensive O serotypes frequently occurring among patients. P. mirabilis exhibited the most intensive swarming growth and was dominating species (86.9%), followed by P. genomospecies, P. vulgaris, and P. penneri. Ninety four per cent strains were recognized as S (smooth) forms. Serological studies (involving ELISA-enzyme-linked immunosorbent assay and Western blotting using native and adsorbed rabbit antisera) enabled classification of 80% S isolates into respective Proteus O serogroups among the 83 ones, described so far. The remaining strains seemed to be serologically unique. Despite the observed big serological variety of Proteus spp. isolates, we found the O78 serogroup recently described in Poland as dominating and identified other widespread serotypes: O3, O6, O10, O11, O27, O28, and O30 reported earlier as predominating also in other countries; O77 and O79 detected lately in Poland; O16, O18, O20, and O50. No unique structural feature of the prevalent O serotypes has been indicated. However, the prevalence of some O serogroups indicates that particular serotypes may be in some ways beneficial to the strains producing these kinds of O antigen.
clinical, strain, O antigen, Proteus, serogroup, Serotypes, ELISA, O serotype
NCBI PubMed ID: 34556711Publication DOI: 10.1038/s41598-021-98228-wJournal NLM ID: 101563288Publisher: London: Nature Publishing Group
Correspondence: dominika.drzewiecka@biol.uni.lodz.pl
Institutions: Department of Biology of Bacteria, Faculty of Biology and Environmental Protection, University of Łódź, Banacha 12/16, 90-237, Łódź, Poland
Methods: ELISA, Western blotting, serological methods, serotyping analysis
- Article ID: 6289
Palusiak A "Proteus mirabilis and Klebsiella pneumoniae as pathogens capable of causing co-infections and exhibiting similarities in their virulence factors" -
Frontiers in Cellular and Infection Microbiology 12 (2022) 991657
The genera Klebsiella and Proteus were independently described in 1885. These Gram-negative rods colonize the human intestinal tract regarded as the main reservoir of these opportunistic pathogens. In favorable conditions they cause infections, often hospital-acquired ones. The activity of K. pneumoniae and P. mirabilis, the leading pathogens within each genus, results in infections of the urinary (UTIs) and respiratory tracts, wounds, bacteremia, affecting mainly immunocompromised patients. P. mirabilis and K. pneumoniae cause polymicrobial UTIs, which are often persistent due to the catheter biofilm formation or increasing resistance of the bacteria to antibiotics. In this situation a need arises to find the antigens with features common to both species. Among many virulence factors produced by both pathogens urease shows some structural similarities but the biggest similarities have been observed in lipids A and the core regions of lipopolysaccharides (LPSs). Both species produce capsular polysaccharides (CPSs) but only in K. pneumoniae these antigens play a crucial role in the serological classification scheme, which in Proteus spp. is based on the structural and serological diversity of LPS O-polysaccharides (OPSs). Structural and serological similarities observed for Klebsiella spp. and Proteus spp. polysaccharides are important in the search for the cross-reacting vaccine antigens.
Lipopolysaccharide, core oligosaccharide, Proteus mirabilis, Klebsiella pneumoniae, virulence factors
NCBI PubMed ID: 36339335Publication DOI: 10.3389/fcimb.2022.991657Journal NLM ID: 101585359Publisher: Lausanne: Frontiers Media SA
Correspondence: A. Palusiak
Institutions: Laboratory of General Microbiology, Department of Biology of Bacteria, Institute of Microbiology, Biotechnology and Immunology, University of Łódź, Łódź, Poland
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5. Compound ID: 1816
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L-Ser2Ac-(1-3)-+
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-4)-b-D-Quip3N-(1-3)-b-D-Ribf-(1-4)-b-D-Galp-(1-3)-a-D-GlcpNAc-(1- |
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Structure type: suggested polymer biological repeating unit
Compound class: O-polysaccharide, O-antigen
Contained glycoepitopes: IEDB_136044,IEDB_137340,IEDB_137472,IEDB_141794,IEDB_141807,IEDB_142078,IEDB_149136,IEDB_150899,IEDB_150900,IEDB_151531,IEDB_190606,SB_137,SB_165,SB_166,SB_187,SB_195,SB_29,SB_7,SB_88
The structure is contained in the following publication(s):
- Article ID: 571
Feng L, Wang W, Tao J, Guo H, Krause G, Beutin L, Wang L "Identification of Escherichia coli O114 O-antigen gene cluster and development of an O114 serogroup-specific PCR assay" -
Journal of Clinical Microbiology 42(8) (2004) 3799-3804
Screening for the Escherichia coli O serotype is the traditional test for identification of E. coli clones. The O-antigen gene cluster of the E. coli O114 type strain was sequenced, and 12 open reading frames were assigned functions on the basis of homology. By screening against all 186 E. coli and Shigella O serotypes, five genes specific to E. coli O114 were identified. A PCR assay based on the O-antigen-specific genes was developed and tested on 41 clinical isolates of E. coli O114. The PCR assay was shown to be highly specific and sensitive. When tested with pork and water samples, as few as 0.12 CFU of E. coli O114 g(-1) were detected. Thus, the PCR assays established in this study can be used to reliably identify E. coli O114 strains and may also be used to detect E. coli O114 strains in food, water, and other environmental samples.
PCR, Escherichia coli, gene cluster, Shigella, Serotypes, O-serotype, O-antigen-specific
NCBI PubMed ID: 15297533Journal NLM ID: 7505564Publisher: American Society for Microbiology
Correspondence: wanglei@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, TEDA College, Nankai University, TEDA, Tianjin 300457, People's Republic of China
Methods: PCR, DNA sequencing
- Article ID: 1778
Knirel YA, Kochetkov NK "The structure of lipopolysaccharides of gram-negative bacteria. III. The structure of O-antigens: A review" -
Biochemistry (Moscow) 59(12) (1994) 1325-1383
This review summarizes data on the composition and structure of the O-antigens, the polysaccharide chains of the outer-membrane lipopolysaccharides (LPS) of Gram-negative bacteria defining the immunospecificity of these microbial cells. Special reference is given to some structural features of the O-antigens, such as the presence of unique monosaccharides and noncarbohydrate components, masked regularity, and the occurrence in one microorganism of LPS with structurally different polysaccharide chains. Antigenic relationships between microorganisms belonging to different taxonomic groups are discussed.
structure, O-antigen, chemical composition, bacterial lipopolysaccharides, Salmonella livingstone C1
NCBI PubMed ID: 7533007Journal NLM ID: 0376536Publisher: Nauka/Interperiodica
Institutions: Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
- Article ID: 2373
Dmitriev BA, L'vov V, Tokhtamysheva NV, Shashkov AS, Kochetkov NK, Jann B, Jann K "Cell wall lipopolysaccharide of Escherichia coli O114:H2. Structure of the polysaccharide chain" -
European Journal of Biochemistry 134 (1983) 517-521
The O-specific polysaccharide of the 0114 antigen (lipopolysaccharide) of Escherichia coli 0114 and oligosaccharides obtained from it by Smith degradation and hydrogen fluoride solvolysis were analyzed, using proton and 13C nuclear magnetic resonance spectroscopy and methylation. The results indicated that the 0114 polysaccharide has the tetrasaccharide repeating unit α-N-acetylglucosamine(1→4)β-3,6-dideoxy-3-(N-acetyl-L-seryl)aminoglucose(1→3)β-ribofuranose(1→4)galactose. In the polysaccharide the repeating units are joined through β1→3-galactosyl linkages. This structure is compared with that of the serologically cross-reacting Shigella boydii 08 antigen and the serological similarity is discussed.
NCBI PubMed ID: 6309515Publication DOI: 10.1111/j.1432-1033.1983.tb07597.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Institut Organicheskoj Khimii imeni N. D. Zelinskogo, Akademiya Nauk S.S.S.R., Leninskij prospekt 47, Moskva, USSR, Max-Planck-Institut für Immunbiologie, Stübeweg 51, D-7800 Freiburg-Zähringen, Federal Republic of Germany
Methods: 13C NMR, 1H NMR, GC-MS
- Article ID: 2684
Knirel YA, Vinogradov EV, Shashkov AS, Sidorczyk Z, Rozalski A, Radziejewska-Lebrecht I, Kaca W "Structural study of O-specific polysaccharides of Proteus" -
Journal of Carbohydrate Chemistry 12 (1993) 379-414
Proteus bacteria are important human opportunistic pathogens which frequently cause urinary tract infections. According to Bergey's Manual of Systematic Bacteriology,1 this genus includes three species: P. mirabilis, P. vulgaris, and P. myxofaciens. A novel species of P. penneri has been recently proposed2,3 for strains formerly called P. vulgaris biogroup I. Proteus is an antigenically heterogeneous group of bacteria, and this is mainly associated with diverse composition and structures of O-specific polysaccharide chains of outer-membrane lipopolysaccharides (O-antigens). The Kauffman-Perch serological classification4 of P. mirabilis and P. vulgaris includes 49 O-serogroups. However, a number of S-strains remain unclassified,5 including strains of P. penneri.
Publication DOI: 10.1080/07328309308019396Journal NLM ID: 8218151Publisher: Marcel Dekker
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky pr. 47, Moscow, B-334, Russia
Methods: 13C NMR, NMR
- Article ID: 3197
Stenutz R, Weintraub A, Widmalm G "The structures of Escherichia coli O-polysaccharide antigens" -
FEMS Microbiology Reviews 30(3) (2006) 382-403
Escherichia coli is usually a non-pathogenic member of the human colonic flora. However, certain strains have acquired virulence factors and may cause a variety of infections in humans and in animals. There are three clinical syndromes caused by E. coli: (i) sepsis/meningitis; (ii) urinary tract infection and (iii) diarrhoea. Furthermore the E. coli causing diarrhoea is divided into different 'pathotypes' depending on the type of disease, i.e. (i) enterotoxigenic; (ii) enteropathogenic; (iii) enteroinvasive; (iv) enterohaemorrhagic; (v) enteroaggregative and (vi) diffusely adherent. The serotyping of E. coli based on the somatic (O), flagellar (H) and capsular polysaccharide antigens (K) is used in epidemiology. The different antigens may be unique for a particular serogroup or antigenic determinants may be shared, resulting in cross-reactions with other serogroups of E. coli or even with other members of the family Enterobacteriacea. To establish the uniqueness of a particular serogroup or to identify the presence of common epitopes, a database of the structures of O-antigenic polysaccharides has been created. The E. coli database (ECODAB) contains structures, nuclear magnetic resonance chemical shifts and to some extent cross-reactivity relationships. All fields are searchable. A ranking is produced based on similarity, which facilitates rapid identification of strains that are difficult to serotype (if known) based on classical agglutinating methods. In addition, results pertinent to the biosynthesis of the repeating units of O-antigens are discussed. The ECODAB is accessible to the scientific community at http://www.casper.organ.su.se/ECODAB/
NMR, structure, serotype, O-antigen, Enterobacteriacea, database
NCBI PubMed ID: 16594963Publication DOI: 10.1111/j.1574-6976.2006.00016.xJournal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: andrej.weintraub@ki.se
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden
- Article ID: 3274
Sidorczyk Z, Swierzko A, Vinogradov EV, Knirel YA, Shashkov AS "Structural and immunochemical studies of the O-specific polysaccharide of Proteus penneri strain 14" -
Archivum Immunologiae et Therapiae Experimentalis 42(3) (1994) 209-215
The complete structure of the O-antigen of Proteus penneri strain 14, containing D-alanine and L-alanine was established using methylation, solvolysis with anhydrous hydrogen fluoride, partial acid hydrolysis, 1H- and 13C-NMR spectroscopy. The role of partial structures of the pentasaccharide repeating unit in manifesting serological specificity and cross-reactivity of this strain with some other bacteria is discussed.
Lipopolysaccharide, structure, role, strain, structural, polysaccharide, O-antigen, repeating unit, O antigen, hydrogen, acid, immunology, O-polysaccharide, bacteria, O-specific, O-specific polysaccharide, Proteus, serological, specificity, Proteus penneri, methylation, spectroscopy, immunochemical, partial structure, pentasaccharide, cross-reactivity, crossreactivity, PDF, solvolysis, hydrogen fluoride, D-alanine, lysis
NCBI PubMed ID: 7487355Journal NLM ID: 0114365Publisher: Basel, Boston: Birkhaüser
Correspondence: zsidor@biol.uni.lodz.pl
Institutions: Institute of Microbiology and Immunology, University of Lodz, Poland.
Methods: 13C NMR, 1H NMR, methylation, GLC-MS, NMR-2D, chemical analysis, mild acid hydrolysis, NMR-1D, serological methods
- Article ID: 3832
Clark CG, Grant CC, Trout-Yakel KM, Tabor H, Ng LK, Rahn K, Franklin K, Kropinski AM "The O28 Antigen Gene Clusters of Salmonella enterica subsp. enterica Serovar Dakar and Serovar Pomona Are Different" -
International Journal of Microbiology 2010 (2010) 209291
A 10 kb O-antigen gene cluster was sequenced from a Salmonella enterica subsp. enterica Dakar O28 reference strain and from two S. Pomona serogroup O28 isolates. The two S. Pomona O antigen gene clusters showed only moderate identity with the S. Dakar O28 gene cluster, suggesting that the O antigen oligosaccharides may contain one or more sugars conferring the O28 epitope but may otherwise be different. These novel findings are absolutely critical for the correct interpretation of molecular serotyping assays targeting genes within the O antigen gene clusters of these Salmonella serotypes and suggest the possibility that the O antigen gene clusters of other Salmonella serovars may also be heterogenous.
O-antigen, gene cluster, serogroup, Salmonella enterica
NCBI PubMed ID: 20652070Journal NLM ID: 101516125Publisher: Hindawi Publishing Corporation
Correspondence: kropinsk@queensu.ca
Institutions: Enteric Diseases Program, Bacteriology and Enteric Diseases Program, National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada R3E 3R2
Methods: genetic methods
- Article ID: 4292
Dziadziuszko H, Kumirska J, Muza S, Czerwicka M, Lubecka EA, Stepnowski P, Kunikowska D "Immunochemical studies of Salmonella Dakar and Salmonella Telaviv O-antigens (serogroup O:28)" -
FEMS Microbiology Letters 326(1) (2012) 55-61
Salmonella Dakar and Salmonella Telaviv bacteria belong to serogroup O:28, which represents 107 serovars and possesses only the epitope O28. Salmonella Telaviv has the subfactors O28(1) and O28(2) , whereas S. Dakar has O28(1) and O28(3) . So far, only limited serological and immunological information for this serogroup is available in the literature. Knowledge of the structures of their O-polysaccharides and the immunochemical investigations performed in this work allowed to reveal the nature of subfactor O28(1) as attributed to the presence of 3-linked (or 3,4-disubstituted) α-D-GalpNAc in the main chains of S. Dakar and S. Telaviv O-polysaccharides. An explanation for the cross-reactions between Salmonella enterica O28 O-antigens and other Salmonella O-polysaccharides and their structural similarity to Escherichia coli O-serogroups is also given.
monoclonal antibody, Serogroup O:28, Salmonella bacterial strains, immunochemical study, O-antigen (OPS), epitope O28
NCBI PubMed ID: 22092663Publication DOI: 10.1111/j.1574-6968.2011.02431.xJournal NLM ID: 7705721Publisher: Blackwell Publishing
Correspondence: kumirska@ chem.univ.gda.pl
Institutions: Department of Molecular Microbiology and Serology, National Salmonella Centre, Medical University of Gdansk, Gdansk, Poland
Methods: periodate oxidation, SDS-PAGE, ELISA, serological methods
- Article ID: 4646
Zhou D, Utkina N, Li D, Dong C, Druzhinina T, Veselovsky V, Liu B "Biochemical characterization of a new b-1,3-galactosyltransferase WbuP from Escherichia coli O114 that catalyzes the second step in O-antigen repeating-unit" -
Carbohydrate Research 381 (2013) 43-50
In this study, synthetic acceptor substrate GlcNAc α-PO3-PO3-(CH2)11-O-phenyl (GlcNAc-PP-PhU) was employed in glycosyl transferase assays to characterize the WbuP galactosyltransferase activity. This activity was time- and enzyme concentration-dependent. The optimal enzyme activity was observed at pH 6.5 and 25°C. The enzyme requires Mn(2+) ions for maximal activity and detergents in the assay did not increase glycosyltransfer activity. The enzyme was shown to be specific for the UDP-Gal donor substrate. Kinetic parameters were determined for UDP-Gal, and GlcNAc-PP-PhU. The enzyme product was determined to have a ?-1,3-linkage using strategies based on exoglycosidase digestion combined with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) as well as collision-induced dissociation electrospray ionization ion trap multiple tandem MS (CID-ESI-IT-MS(n)). Our results conclusively demonstrate that the wbuP gene of Escherichia coli O114 encodes a UDP-Gal: GlcNAc ?-pyrophosphate-lipid ?-1,3-Gal-transferase that transfers the second sugar moiety in the assembly of the O114 repeating unit.
Escherichia coli, mass spectrometry, glycosyl transferase, Functional characterization, Escherichia coli O-antigen
NCBI PubMed ID: 24056013Publication DOI: 10.1016/j.carres.2013.08.021Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: daweizhou@nankai.edu.cn
Institutions: TEDA School of Biological Sciences and Biotechnology, Nankai University, 23 HongDa Street, TEDA, Tianjin, China
Methods: PCR, GC-MS, SDS-PAGE, glycosyltransferase assays, kinetics assays, ESI-MS, MALDI-TOF MS, CID-MS/MS, biochemical methods
- Article ID: 5472
Liu B, Furevi A, Perepelov AV, Guo X, Cao H, Wang Q, Reeves PR, Knirel YA, Wang L, Widmalm G "Structure and genetics of Escherichia coli O antigens" -
FEMS Microbiology Reviews 44(6) (2020) 655-683
Escherichia coli includes clonal groups of both commensal and pathogenic strains, with some of the latter causing serious infectious diseases. O antigen variation is current standard in defining strains for taxonomy and epidemiology, providing the basis for many serotyping schemes for Gram-negative bacteria. This review covers the diversity in E. coli O antigen structures and gene clusters, and the genetic basis for the structural diversity. Of the 187 formally defined O antigens, six (O31, O47, O67, O72, O94 and O122) have since been removed and four (O14, O34, O89 and O144) strains do not produce any O antigen. Therefore, structures are presented for 176 of the 181 E. coli O antigens, some of which include subgroups. Most (93%) of these O antigens are synthesized via the Wzx/Wzy pathway, 11 via the ABC transporter pathway, with O20, O57 and O60 still uncharacterized due to failure to find their O antigen gene clusters. Biosynthetic pathways are given for 38 of the 49 sugars found in E. coli O antigens, and several pairs or groups of the E. coli antigens that have related structures show close relationships of the O antigen gene clusters within clades, thereby highlighting the genetic basis of the evolution of diversity.
structure, O antigen, Escherichia coli, gene cluster, serogroup, diversity
NCBI PubMed ID: 31778182Publication DOI: 10.1093/femsre/fuz028Journal NLM ID: 8902526Publisher: Oxford University Press
Correspondence: G. Widmalm
; Lei Wang
Institutions: Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University, Stockholm, Sweden, N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Tianjin Key Laboratory of Microbial Functional Genomics, Tianjin, China, The Key Laboratory of Molecular Microbiology and Technology, Ministry of Education, Tianjin, China, School of Molecular and Microbial Bioscience (G08), University of Sydney, Sydney, Australia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, China, Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
- Article ID: 6301
Qin CJ, Ding MR, Tian GZ, Zou XP, Fu JJ, Hu J, Yin J "Chemical approaches towards installation of rare functional groups in bacterial surface glycans" -
Chinese Journal of Natural Medicines = Zhongguo Tianran Yaowu 20(6) (2022) 401-420
Bacterial surface glycans perform a diverse and important set of biological roles, and have been widely used in the treatment of bacterial infectious diseases. The majority of bacterial surface glycans are decorated with diverse rare functional groups, including amido, acetamidino, carboxamido and pyruvate groups. These functional groups are thought to be important constituents for the biological activities of glycans. Chemical synthesis of glycans bearing these functional groups or their variants is essential for the investigation of structure-activity relationships by a medicinal chemistry approach. To date, a broad choice of synthetic methods is available for targeting the different rare functional groups in bacterial surface glycans. This article reviews the structures of naturally occurring rare functional groups in bacterial surface glycans, and the chemical methods used for installation of these groups.
chemical synthesis, acetamidino group, amido group, bacterial surface glycan, carboxamido group, pyruvyl ketal
NCBI PubMed ID: 35750381Publication DOI: 10.1016/S1875-5364(22)60177-8Journal NLM ID: 101504416Publisher: Beijing: Science Press; Elsevier
Correspondence: J. Yin
Institutions: Key Laboratory of Carbohydrate Chemistry and Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, China, Wuxi School of Medicine, Jiangnan University, Wuxi, China
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6. Compound ID: 2066
|
a-Murp2Ac-(1-3)-+
|
-4)-b-D-GlcpNAc-(1-4)-a-D-GalpA-(1-4)-b-L-Rhap-(1-
|
Ser-(1-6)-+ |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 671
Gunawardena S, Reddy GP, Wang YH, Kolli VSK, Orlando R, Morris JG, Bush CA "Structure of a muramic acid containing capsular polysaccharide from the pathogenic strain of Vibrio vulnificus ATCC27562" -
Carbohydrate Research 309(1) (1998) 65-76
Vibrio vulnificus strains isolated from septicemia cases and from the environment show a wide variety of capsular types. In an attempt to find common structural features which can be correlated with pathogenicity and toxicity, we have determined structures of the capsular polysaccharides (CPS) from several pathogenic strains. We report the complete structure of the polysaccharide from the pathogenic V. vulnificus strain ATCC27562 using a combination of homonuclear and heteronuclear one-dimensional and two dimensional NMR experiments. The 13C and 1H NMR spectra, including the exchangeable amide proton resonances, have been completely assigned. The amide linkage between Ser and C6 of GalA has been unambiguously determined by water-suppressed 2D NOESY. To verify the structure established by NMR, we have fragmented the polymer employing the Smith degradation procedure. The Smith product identified by NMR and matrix-assisted laser desorption mass spectrometry is consistent with the proposed structure for the CPS, which is composed of D-GlcNAc, MurNAc, D-GalA, L-Rha and is serine-linked as shown: [formula: see text]
structure, mass spectrometry, Vibrio, Capsular polysaccaride, NMR spectrometry
NCBI PubMed ID: 9720237Publication DOI: 10.1016/s0008-6215(98)00115-3Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21250, USA, Complex carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore, MD 21201, USA
Methods: NMR-2D, NMR, Smith degradation
- Article ID: 5791
Knirel YA, Van Calsteren M "Bacterial exopolysaccharides" -
Book: Comprehensive Glycoscience: From Chemistry to Systems Biology. Reference Module in Chemistry, Molecular Sciences and Chemical Engineering (2021) 1-75
Bacterial extracellular polysaccharides are known as a cell-bound capsule, a sheath, or a slime, which is excreted into the environment. They play an important role in virulence of medical bacteria and plant-to-symbiont interaction and are used for serotyping of bacteria and production of vaccines. Some exopolysaccharides have commercial applications in industry, and claims of health benefits have been documented for an increasing number of them. Exopolysaccharides have diverse composition and structure, and some contain sugar and non-sugar components that are found in bacterial carbohydrates only. The present article provides an updated collection of the data on exopolysaccharides of various classes of gram-negative and gram-positive bacteria reported until the end of 2019. When known, biosynthesis pathways of exopolysaccharides are treated in a summary manner. References are made to structure and biosynthesis relatedness between exopolysaccharides of different bacterial taxa as well as between bacterial polysaccharides and mammalian glycosaminoglycans.
polysaccharide structure, Gram-negative bacteria, capsule, Biofilm, polysaccharide biosynthesis, gram-positive bacteria, Monosaccharide composition, Bacterial exopolysaccharide, non-sugar component
Publication DOI: 10.1016/B978-0-12-819475-1.00005-5Publisher: Elsevier
Correspondence: marie-rose.vancalsteren@canada.ca; yknirel@gmail.com
Editors: Barchi J, Kamerling H
Institutions: N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, Saint-Hyacinthe Research and Development Centre, Agriculture and Agri-Food Canada, Saint-Hyacinthe, QC, Canada
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7. Compound ID: 2150
|
a-Murp2Ac-(1-3)-+
|
b-D-GlcpNAc-(1-4)-a-D-GalpA-(1-2)-Suga
|
Ser-(1-6)-+
Sug = unidentified tetritol = SMILES OC{2}C(C(CO)O)O |
Show graphically |
Structure type: oligomer
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531
The structure is contained in the following publication(s):
- Article ID: 671
Gunawardena S, Reddy GP, Wang YH, Kolli VSK, Orlando R, Morris JG, Bush CA "Structure of a muramic acid containing capsular polysaccharide from the pathogenic strain of Vibrio vulnificus ATCC27562" -
Carbohydrate Research 309(1) (1998) 65-76
Vibrio vulnificus strains isolated from septicemia cases and from the environment show a wide variety of capsular types. In an attempt to find common structural features which can be correlated with pathogenicity and toxicity, we have determined structures of the capsular polysaccharides (CPS) from several pathogenic strains. We report the complete structure of the polysaccharide from the pathogenic V. vulnificus strain ATCC27562 using a combination of homonuclear and heteronuclear one-dimensional and two dimensional NMR experiments. The 13C and 1H NMR spectra, including the exchangeable amide proton resonances, have been completely assigned. The amide linkage between Ser and C6 of GalA has been unambiguously determined by water-suppressed 2D NOESY. To verify the structure established by NMR, we have fragmented the polymer employing the Smith degradation procedure. The Smith product identified by NMR and matrix-assisted laser desorption mass spectrometry is consistent with the proposed structure for the CPS, which is composed of D-GlcNAc, MurNAc, D-GalA, L-Rha and is serine-linked as shown: [formula: see text]
structure, mass spectrometry, Vibrio, Capsular polysaccaride, NMR spectrometry
NCBI PubMed ID: 9720237Publication DOI: 10.1016/s0008-6215(98)00115-3Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County 21250, USA, Complex carbohydrate Research Center and Department of Biochemistry and Molecular Biology, The University of Georgia, 220 Riverbend Road, Athens, GA 30602-4712, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore, MD 21201, USA
Methods: NMR-2D, NMR, Smith degradation
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8. Compound ID: 3122
|
a-Mur2Ac-(1-3)-+
|
-4)-a-D-GlcpNAc-(1-4)-a-D-GalpA-(1-4)-b-L-Rhap-(1-
|
L-Ser-(2-6)-+ |
Show graphically |
Structure type: polymer chemical repeating unit
Contained glycoepitopes: IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1136
Reddy GP, Hayat U, Xu QW, Reddy KV, Wang YH, Chiu KW, Morris JG, Bush CA "Structure determination of the capsular polysaccharide from Vibrio vulnificus strain 6353" -
European Journal of Biochemistry 255(1) (1998) 279-288
Vibrio vulnificus is a pathogenic gram-negative bacterium, endemic to brackish waters, which is often isolated from sediments, from the water column or from shellfish. It is associated with wound infections and septicemia in humans and the virulence of V. vulnificus has been strongly associated with encapsulation. The capsular polysaccharide purified from a virulent strain of V. vulnificus 6353 did not show cross reactivity with antibodies to the capsular polysaccharide of a related pathogenic strain of V. vulnificus (MO6-24) the structure of which was recently reported. NMR spectroscopic analysis of the purified polysaccharide from strain 6353 showed that the polymer is composed of four sugar residues per repeating subunit including 2,6-dideoxy-2-N-acetylamino-α-D-glucose (QuiNAc), 2-deoxy-2-N-acetylamino-α-D-galactose (α-D-GalNAc), 2-deoxy-2-N-acetylamino-α-D-galcturonic acid (α-D-GalNAcA) and 2-N-acetylamino-α-D-glucuronamide (α-D-GlcNAcANH2). The 1H- and 13C NMR spectra were completely assigned by homonuclear and heteronuclear NMR spectroscopy. Sugar types and anomeric configurations were determined from proton homonuclear coupling constants and glycosidic linkages were determined from 1H-13C heteronuclear multiple bond correlation spectra. Sugar identities were confirmed by high performance anion-exchange chromatography and absolute configurations were determined by gas chromatography in combination with molecular modeling and NMR spectroscopy. The structure of the polysaccharide repeating unit is: [→4)-α-D-GalpNAc-(1→3)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc-(1→]n α-D-GlcpNAcANH2(1→4)-→. While there are some common features shared among the structures of the capsular polysaccharides of pathogenic strains of V. vulnificus, there are distinct differences in the detailed structures.
NMR, structure, polysaccharide, bacteria, Vibrio, Vibrio vulnificus
NCBI PubMed ID: 9692929Publication DOI: 10.1046/j.1432-1327.1998.2550279.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore MD, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore MD, USA
Methods: 13C NMR, 1H NMR, NMR-2D, HPLC
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9. Compound ID: 3123
|
a-Mur2Ac-(1-3)-+
|
-4)-b-D-GlcpNAc-(1-4)-a-D-GalpA-(1-4)-b-L-Rhap-(1-
|
L-Ser-(2-6)-+ |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS
Contained glycoepitopes: IEDB_135813,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_225177,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1136
Reddy GP, Hayat U, Xu QW, Reddy KV, Wang YH, Chiu KW, Morris JG, Bush CA "Structure determination of the capsular polysaccharide from Vibrio vulnificus strain 6353" -
European Journal of Biochemistry 255(1) (1998) 279-288
Vibrio vulnificus is a pathogenic gram-negative bacterium, endemic to brackish waters, which is often isolated from sediments, from the water column or from shellfish. It is associated with wound infections and septicemia in humans and the virulence of V. vulnificus has been strongly associated with encapsulation. The capsular polysaccharide purified from a virulent strain of V. vulnificus 6353 did not show cross reactivity with antibodies to the capsular polysaccharide of a related pathogenic strain of V. vulnificus (MO6-24) the structure of which was recently reported. NMR spectroscopic analysis of the purified polysaccharide from strain 6353 showed that the polymer is composed of four sugar residues per repeating subunit including 2,6-dideoxy-2-N-acetylamino-α-D-glucose (QuiNAc), 2-deoxy-2-N-acetylamino-α-D-galactose (α-D-GalNAc), 2-deoxy-2-N-acetylamino-α-D-galcturonic acid (α-D-GalNAcA) and 2-N-acetylamino-α-D-glucuronamide (α-D-GlcNAcANH2). The 1H- and 13C NMR spectra were completely assigned by homonuclear and heteronuclear NMR spectroscopy. Sugar types and anomeric configurations were determined from proton homonuclear coupling constants and glycosidic linkages were determined from 1H-13C heteronuclear multiple bond correlation spectra. Sugar identities were confirmed by high performance anion-exchange chromatography and absolute configurations were determined by gas chromatography in combination with molecular modeling and NMR spectroscopy. The structure of the polysaccharide repeating unit is: [→4)-α-D-GalpNAc-(1→3)-α-D-GalpNAcA-(1→3)-α-D-QuipNAc-(1→]n α-D-GlcpNAcANH2(1→4)-→. While there are some common features shared among the structures of the capsular polysaccharides of pathogenic strains of V. vulnificus, there are distinct differences in the detailed structures.
NMR, structure, polysaccharide, bacteria, Vibrio, Vibrio vulnificus
NCBI PubMed ID: 9692929Publication DOI: 10.1046/j.1432-1327.1998.2550279.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Correspondence: bush@umbc.edu
Institutions: Department of Chemistry and Biochemistry, University of Maryland Baltimore County, Baltimore MD, USA, Departments of Medicine and Pathology, University of Maryland School of Medicine and Veterans Affairs Medical Center, Baltimore MD, USA
Methods: 13C NMR, 1H NMR, NMR-2D, HPLC
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10. Compound ID: 3363
Structure type: monomer
Aglycon: polyacrylamide
Contained glycoepitopes: IEDB_150900
The structure is contained in the following publication(s):
- Article ID: 1235
Sidorczyk Z, Swierzko A, Knirel YA, Vinogradov EV, Chernyak AY, Kononov LO, Cedzynski M, Rozalski A, Kaca W, Shashkov AS, Kochetkov NK "Structure and epitope specificity of the O-specific polysaccharide of Proteus penneri strain 12 (ATCC 33519) containing the amide of D-galacturonic acid with L-threonine" -
European Journal of Biochemistry 230 (1995) 713-721
O-specific polysaccharide was isolated from Proteus penneri strain 12 (ATCC 33519) lipopolysaccharide (LPS) and studied using NMR spectroscopy, including selective spin-decoupling, one-dimensional NOE, two-dimensional homonuclear correlation spectroscopy, 13C,1H heteronuclear correlation spectroscopy and chemical methods (O-deacetylation, Smith degradation, partial acid hydrolysis followed by borohydride reduction and methylation). The amide of D-galacturonic acid with L-threonine [D-GalA(L-Thr)] was identified as a constituent of the polysaccharide and the following structure of the tetrasaccharide repeating unit was established: [formula: see text] where the degree of O-acetylation at either position varies over 20-40%. Serological study with LPS, its degradation products and related synthetic glycoconjugates (2-acrylamidoethyl glycosides of amides of α-D-GalA with L-amino acids copolymerised with acrylamide) showed that D-GalA(L-Thr) plays an important role in manifesting the serological specificity of the P. penneri 12 O-antigen. Serological cross reactions between LPSs of P. penneri 12 and Proteus mirabilis S1959, R14/S1959 (transient-like form), O23 and O28 are discussed.
Lipopolysaccharide, structure, O-antigen, epitope, Proteus mirabilis, Proteus penneri
NCBI PubMed ID: 7541754Publication DOI: 10.1111/j.1432-1033.1995.0713h.xJournal NLM ID: 0107600Publisher: Oxford, UK: Blackwell Science Ltd. on behalf of the Federation of European Biochemical Societies
Institutions: Institute of Microbiology and Immunology, University of Lodz, Poland, Center of Microbiology and Virology, Polish Academy of Sciences, Lodz, Poland, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
Methods: NMR
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11. Compound ID: 3602
|
L-Ser-(2-6)-+
|
-4)-b-D-GlcpA-(1-4)-a-D-GlcpNAc-(1-6)-a-D-GlcpNAc-(1- |
Show graphically |
Structure type: polymer chemical repeating unit
Compound class: CPS, K-antigen
Contained glycoepitopes: IEDB_115136,IEDB_137340,IEDB_140630,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_423153
The structure is contained in the following publication(s):
- Article ID: 1352
Amor PA, Yethon JA, Monteiro MA, Whitfield C "Assembly of the K40 antigen in Escherichia coli: Identification of a novel enzyme responsible for addition of L-serine residues to the glycan backbone and its requirement for K40 polymerization" -
Journal of Bacteriology 181(3) (1999) 772-780
Escherichia coli O8:K40 coexpresses two distinct lipopolysaccharide (LPS) structures on its surface. The O8 polysaccharide is a mannose homopolymer with a trisaccharide repeat unit and is synthesized by an ABC-2 transport-dependent pathway. The K40LPS backbone structure is composed of a trisaccharide repeating unit of N-acetylglucosamine (GlcNAc) and glucuronic acid (GlcA) and has an uncommon substitution, an L-serine moiety attached to glucuronic acid. The gene cluster responsible for synthesis of the K40 polysaccharide has previously been cloned and sequenced and was found to contain six open reading frames (ORFs) (P. A. Amor and C. Whitfield, Mol. Microbiol. 26:145-161, 1997). Here, we demonstrate that insertional inactivation of orf1 results in the accumulation of a semirough (SR)-K40LPS form which retains reactivity with specific polyclonal serum in Western immunoblots. Structural and compositional analysis of the SR-K40LPS reveals that it comprises a single K40 repeat unit attached to lipid A core. The lack of polymerization of the K40 polysaccharide indicates that orf1 encodes the K40 polymerase (Wzy) and that assembly of the K40 polysaccharide occurs via a Wzy-dependent pathway (in contrast to that of the O8 polysaccharide). Inactivation of orf3 also results in the accumulation of an SR-LPS form which fails to react with specific polyclonal K40 serum in Western immunoblots. Methylation linkage analysis and fast atom bombardment-mass spectrometry of this SR-LPS reveals that the biological repeat unit of the K40 polysaccharide is GlcNAc-GlcA-GlcNAc. Additionally, this structure lacks the L-serine substitution of GlcA. These results show that (i) orf3 encodes the enzyme responsible for the addition of the L-serine residue to the K40 backbone and (ii) substitution of individual K40 repeats with L-serine is essential for their recognition and polymerization into the K40 polysaccharide by Wzy.
biosynthesis, antigen, Escherichia, Escherichia coli, glycan, requirement, assembly, identification, backbone, enzyme, polymerization, L-serine
NCBI PubMed ID: 9922239Journal NLM ID: 2985120RPublisher: American Society for Microbiology
Correspondence: cwhitfie@uoguelph.ca
Institutions: Department of Microbiology, University of Guelph, Guelph, Ontario N1G 2W1, Canada, Institute for Biological Sciences, National Research Council of Canada, Ottawa, Ontario K1A 0R6, Canada
Methods: genetic methods
- Article ID: 2063
Dengler T, Jann B, Jann K "Structure of the serine-containing capsular polysaccharide K40 antigen from Escherichia coli O8:K40:H9" -
Carbohydrate Research 150 (1986) 233-240
The structure of the K40 antigenic capsular polysaccharide (K40 antigen) of E. coli O8:K40:H9 was elucidated by determination of the composition, 1H- and 13C-n.m.r. spectroscopy, periodate oxidation and Smith degradation, and methylation analysis. The K40 polysaccharide consists of [(O-β-D-glucopyranosyluronic acid)-(1→4)-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-(1→6)-O-(2-acetamido-2-deoxy-α-D-glucopyranosyl)-(1→4)] repeating units. All of the glucuronic acid residues are substituted amidically with L-serine.
structure, capsular polysaccharide, Escherichia coli K40
NCBI PubMed ID: 3093075Publication DOI: 10.1016/0008-6215(86)80019-2Journal NLM ID: 0043535Publisher: Elsevier
Institutions: Max-Planck-Institut für Immunbiologie, D-7800 Freiburg F.R.G.
- Article ID: 3259
Whitfield C "Biosynthesis and Assembly of Capsular Polysaccharides in Escherichia coli" -
Annual Review of Biochemistry 75(1) (2006) 39-68
Capsules are protective structures on the surfaces of many bacteria. The remarkable structural diversity in capsular polysaccharides is illustrated by almost 80 capsular serotypes in Escherichia coli. Despite this variation, the range of strategies used for capsule biosynthesis and assembly is limited, and E. coli isolates provide critical prototypes for other bacterial species. Related pathways are also used for synthesis and export of other bacterial glycoconjugates and some enzymes/processes have counterparts in eukaryotes. In gram-negative bacteria, it is proposed that biosynthesis and translocation of capsular polysaccharides to the cell surface are temporally and spatially coupled by multiprotein complexes that span the cell envelope. These systems have impact on both a general understanding of membrane trafficking in bacteria and on bacterial pathogenesis. Expected online publication date for the Annual Review of Biochemistry Volume 75 is June 2, 2006. Please see http://www.annualreviews.org/catalog/pub_dates.asp for revised estimates.
glycosyltransferases, cell-surface biogenesis, trans-envelope assembly complex, polysaccharide export
NCBI PubMed ID: 16756484Publication DOI: 10.1146/annurev.biochem.75.103004.142545Journal NLM ID: 2985150RCorrespondence: cwhitfie@uoguelph.ca
Institutions: Department of Molecular and Cellular Biology, University of Guelph, Guelph, Ontario N1G 2W1 Canada
- Article ID: 4879
Perepelov AV, Guo X, Senchenkova SN, Li Y, Shashkov AS, Liu B, Knirel YA "Structure and gene cluster of the O-antigen of Escherichia coli O137" -
Carbohydrate Research 422 (2016) 13-16
The O-polysaccharide (O-antigen) was isolated from the lipopolysaccharide of Escherichia coli O137 and studied by sugar analysis and NMR spectroscopy. The following structure of the branched tetrasaccharide repeating unit was established: Formula: see text] Both structure and gene cluster of the E. coli O137 polysaccharide are related to those of the E. coli K40 polysaccharide (Amor et al., 1999), which lacks the side-chain glucosylation but contains serine that is amide-linked to GlcA. Functions of genes in the O137-antigen gene cluster were assigned by a comparison with those in K40 and sequences in the available databases. Particularly, predicted glycosyltransferases encoded in the gene cluster were assigned to the formation of three glycosidic linkages in the O-polysaccharide repeating unit.
Lipopolysaccharide, O-antigen, Escherichia coli, bacterial polysaccharide structure, O-antigen gene cluster
Publication DOI: 10.1016/j.carres.2016.01.002Journal NLM ID: 0043535Publisher: Elsevier
Correspondence: perepel@ioc.ac.ru
Institutions: N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia, TEDA Institute of Biological Sciences and Biotechnology, Nankai University, TEDA, Tianjin, 300457, China, The Third Central Hospital of Tianjin, Hedong District, Tianjin 300170, China
Methods: 13C NMR, 1H NMR, NMR-2D, sugar analysis, acid hydrolysis, GLC, GPC, mild acid degradation, function analysis of gene clusters
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12. Compound ID: 3759
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D-Ala-(2-1)-L-Ala-(2-5)-+
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b-D-GlcpNAc-(1-4)-b-Murp2Ac-(?-2)-L-Ser-(1-2)-D-Glu-(5-2)-L-Ala-(1-2)-D-Ala-(1-6)-L-Lys-(2-1)-L-Lys-(?-1)-Gly-(2-1)-D-Glu-(2-1)-L-Ser-(2-8)-+
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-4)-b-D-GlcpNAc-(1-4)-b-Murp2Ac-(1- |
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Structure type: fragment of a bigger structure
Trivial name: murein
Compound class: cell wall polysaccharide
Contained glycoepitopes: IEDB_135813,IEDB_136017,IEDB_137340,IEDB_141807,IEDB_150900,IEDB_151531,IEDB_1635957,IEDB_241115,IEDB_423183,IEDB_885814
The structure is contained in the following publication(s):
- Article ID: 1432
Schubert K, Fiedler F "Structural investigations on the cell surface of Erysipelothrix rhusiopathiae" -
Systematic and Applied Microbiology 24(1) (2001) 26-30
The cell wall of Erysipelothrix rhusiopathiae was investigated. The corrected structure of the murein, which was published earlier, is reported here. The murein belongs to the B1δ type. It has L-alanine in position three of the peptide subunit and is crosslinked via a glycine-L-lysine-L-lysine interpeptide bridge. As expected by the complex serological situation in E. rhusiopathiae the carbohydrate moiety of the cell wall proofed to be very intricate. As accessory polymers polysaccharide(s) and teichoic acid(s) were identified. The teichoic acid(s) possess two novel polyols of which one could not be identified, the other one behaved like 6-O-methylgalactitol in gas liquid chromatography. Glucose and N-acetylgalactosamine were determined as substituents. The polysaccharide(s) is composed of mainly N-acetylfucosamine and smaller amounts of galactose, N- acetylglucosamine, and a further unidentified sugar appearing later than hexaacetylsorbitol in GLC.
serology, polysaccharides, teichoic acid, murein, Erysipelothrix rhusiopathiae
NCBI PubMed ID: 11403395Publication DOI: 10.1078/0723-2020-00010Journal NLM ID: 8306133Correspondence: K.Schubert@lrz.uni-muenchen.de
Institutions: Institut fur Genetik und Mikrobiologie der Universitat Munchen, Munich, Germany
Methods: partial acid hydrolysis, TLC, GLC, paper chromatography, HF treatment, hydrazinolysis
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13. Compound ID: 3825
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Lau-(1-2)-+
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LIP-(1-2)-+ a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-+
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a-L-6dTalp3Me-(1-3)-L-Ser-(1-2)-L-Ser3(%)Me-(1-2)-L-Phe-(1-2)-D-aThr1Me |
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Structure type: oligomer
Trivial name: GPL-I
Compound class: glycopeptidolipid (GPL)
Contained glycoepitopes: IEDB_136105,IEDB_150900,IEDB_225177,IEDB_534864,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1451
Chatterjee D, Khoo KH "The surface glycopeptidolipids of mycobacteria: structures and biological properties" -
Cellular and Molecular Life Sciences 58(14) (2001) 2018-2042
One of the most important opportunistic pathogens associated with acquired immunodeficiency syndrome (AIDS) is the M. avium complex. M. avium infections are found in up to 70% of individuals in advanced stages of AIDS. It is apparent that M. avium can replicate in host macrophages and persist for long periods. This group of mycobacteria are distinguished by the presence of unique, highly antigenic, surface- located lipids known as the glycopeptidolipids (GPLs). The GPLs are the chemical basis of the 31 distinct serovars of the M. avium complex, and have also been identified in some other species. The M. avium lipids are immunosuppressive and can induce a variety of cytokines that affect general host responses. Despite extensive chemical characterization of the structures of these GPLs, much work is needed to elucidate the molecular mechanism involved in this complex glycosylation pathway and its genetic basis. The challenges for the future lie in explaining the roles of these copious products in the intracellular life and infectivity of mycobacteria. The intention of our review is to offer a concise account of the structures of the M. avium lipids, their putative roles in the host responses, bacterial physiology and pathogenesis, particularly in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). Advances in chemical synthesis of the various haptenic oligosaccharides are also given to demonstrate how these have helped to define the immunogenic determinants. We believe that future research should involve the creation of conditional mutants defective in these lipids for both functional and biosynthesis studies which will complement biological assays using chemically defined or modified neoglycoconjugates
Mycobacteria, neoglycoproteins, glycopeptidolipid (GPL), Mycobacterium avium complex (MAC), haptenic oligosaccharides
NCBI PubMed ID: 11814054Publication DOI: 10.1007/PL00000834Journal NLM ID: 9705402Publisher: Basel: Springer
Correspondence: delphi@lamar.colostate.edu
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA, Institute of Biological Chemistry, Academia Sinica, Taipei (Taiwan)
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14. Compound ID: 3826
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Lau-(1-2)-+
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LIP-(1-2)-+ a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-+
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a-L-6dTalp2Ac3Me-(1-3)-L-Ser-(1-2)-L-Ser3(%)Me-(1-2)-L-Phe-(1-2)-D-aThr1Me |
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Structure type: oligomer
Trivial name: GPL-II
Compound class: glycopeptidolipid (GPL)
Contained glycoepitopes: IEDB_136105,IEDB_150900,IEDB_225177,IEDB_534864,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1451
Chatterjee D, Khoo KH "The surface glycopeptidolipids of mycobacteria: structures and biological properties" -
Cellular and Molecular Life Sciences 58(14) (2001) 2018-2042
One of the most important opportunistic pathogens associated with acquired immunodeficiency syndrome (AIDS) is the M. avium complex. M. avium infections are found in up to 70% of individuals in advanced stages of AIDS. It is apparent that M. avium can replicate in host macrophages and persist for long periods. This group of mycobacteria are distinguished by the presence of unique, highly antigenic, surface- located lipids known as the glycopeptidolipids (GPLs). The GPLs are the chemical basis of the 31 distinct serovars of the M. avium complex, and have also been identified in some other species. The M. avium lipids are immunosuppressive and can induce a variety of cytokines that affect general host responses. Despite extensive chemical characterization of the structures of these GPLs, much work is needed to elucidate the molecular mechanism involved in this complex glycosylation pathway and its genetic basis. The challenges for the future lie in explaining the roles of these copious products in the intracellular life and infectivity of mycobacteria. The intention of our review is to offer a concise account of the structures of the M. avium lipids, their putative roles in the host responses, bacterial physiology and pathogenesis, particularly in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). Advances in chemical synthesis of the various haptenic oligosaccharides are also given to demonstrate how these have helped to define the immunogenic determinants. We believe that future research should involve the creation of conditional mutants defective in these lipids for both functional and biosynthesis studies which will complement biological assays using chemically defined or modified neoglycoconjugates
Mycobacteria, neoglycoproteins, glycopeptidolipid (GPL), Mycobacterium avium complex (MAC), haptenic oligosaccharides
NCBI PubMed ID: 11814054Publication DOI: 10.1007/PL00000834Journal NLM ID: 9705402Publisher: Basel: Springer
Correspondence: delphi@lamar.colostate.edu
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA, Institute of Biological Chemistry, Academia Sinica, Taipei (Taiwan)
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15. Compound ID: 3827
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Lau-(1-2)-+
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/Variants 0/-a-L-Rhap-(1-3)-a-L-Rhap-(1-3)-+
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LIP-(1-2)-+ |
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a-L-6dTalp3Me-(1-3)-L-Ser-(1-2)-L-Ser3(%)Me-(1-2)-L-Phe-(1-2)-D-aThr1Me
/Variants 0/ is:
Oco-(1-4)-
OR (exclusively)
Dco-(1-4)- |
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Structure type: oligomer
Trivial name: GPL-III
Compound class: glycopeptidolipid (GPL)
Contained glycoepitopes: IEDB_136105,IEDB_150900,IEDB_225177,IEDB_534864,IEDB_885823
The structure is contained in the following publication(s):
- Article ID: 1451
Chatterjee D, Khoo KH "The surface glycopeptidolipids of mycobacteria: structures and biological properties" -
Cellular and Molecular Life Sciences 58(14) (2001) 2018-2042
One of the most important opportunistic pathogens associated with acquired immunodeficiency syndrome (AIDS) is the M. avium complex. M. avium infections are found in up to 70% of individuals in advanced stages of AIDS. It is apparent that M. avium can replicate in host macrophages and persist for long periods. This group of mycobacteria are distinguished by the presence of unique, highly antigenic, surface- located lipids known as the glycopeptidolipids (GPLs). The GPLs are the chemical basis of the 31 distinct serovars of the M. avium complex, and have also been identified in some other species. The M. avium lipids are immunosuppressive and can induce a variety of cytokines that affect general host responses. Despite extensive chemical characterization of the structures of these GPLs, much work is needed to elucidate the molecular mechanism involved in this complex glycosylation pathway and its genetic basis. The challenges for the future lie in explaining the roles of these copious products in the intracellular life and infectivity of mycobacteria. The intention of our review is to offer a concise account of the structures of the M. avium lipids, their putative roles in the host responses, bacterial physiology and pathogenesis, particularly in immunocompromised patients such as those infected with human immunodeficiency virus (HIV). Advances in chemical synthesis of the various haptenic oligosaccharides are also given to demonstrate how these have helped to define the immunogenic determinants. We believe that future research should involve the creation of conditional mutants defective in these lipids for both functional and biosynthesis studies which will complement biological assays using chemically defined or modified neoglycoconjugates
Mycobacteria, neoglycoproteins, glycopeptidolipid (GPL), Mycobacterium avium complex (MAC), haptenic oligosaccharides
NCBI PubMed ID: 11814054Publication DOI: 10.1007/PL00000834Journal NLM ID: 9705402Publisher: Basel: Springer
Correspondence: delphi@lamar.colostate.edu
Institutions: Department of Microbiology, Colorado State University, Fort Collins 80523, USA, Institute of Biological Chemistry, Academia Sinica, Taipei (Taiwan)
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